HBV aptamer

May 6, 2024 • Jiali Wang, Fu Bo

Description

In 2011, Feng H, Beck J, Nassal M, Hu KH selexd aptamers targeting human hepatitis B virus (HBV) RNA packaging signals using the SELEX method. These aptamers can mimic the specific interaction between HBV polymerase (P protein) and the ε RNA stem ring structure on pgRNA, but do not support viral replication. Especially, the S9 aptamer has shown high affinity and specificity for recombinant truncated HBV P protein (miniP) in vitro experiments, and does not support viral replication when used as part of the complete HBV genome. Introducing S9 RNA into HepG2 cells that briefly produce HBV strongly inhibited the packaging and DNA synthesis of pgRNA, indicating that S9 RNA can act as an ε bait to competitively inhibit the binding of P protein to the real ε signal on pgRNA. This study demonstrates the successful identification of human HBV ε - aptamers using the in vitro SELEX method, and that S9 aptamers effectively inhibit HBV replication, providing a theoretical basis for the formation of ε - bait RNA interference virus P - ε complexes, and suggesting that S9 class RNA may be further developed as a useful therapeutic tool for chronic hepatitis B^[1].

SELEX

In 2011, Feng H, Beck J, Nassal M, Hu KH used an in vitro reconstruction system based on recombinant truncated HBV P protein (miniP) to screen potential e-structure aptamers from two large, randomized upper stem e-RNA pools. These RNA pools are enriched with RNAs strongly bound to miniPs through three rounds of screening. Through RT-PCR product cloning, 45 individual clones were randomly selected from approximately 500 clones for sequencing. Most (43 of 45) carry upper stem sequences highly enriched in adenosine (A). The selected aptamers S6 and S9 showed high affinity and specificity for miniPs in vitro. S9 RNA strongly inhibits the packaging and DNA synthesis of pgRNA, indicating that S9 RNA can act as a decoy for the e structure by competitively inhibiting the binding of P protein to the real e signal on pgRNA^[1].
Detailed information are accessible on SELEX page.

Structure

The 2D structure of the figure is based on the article by ribodraw tool to draw. S9 apatmer binds to hepatitis B virus (HBV) polymerase (P protein) (miniP)^[1].

5'-UGUUCAUGUCCUACUGUUCAAACAAAAAAACUGUGCACAAAAAUAAAUUGGGGCAUGGACA-3'

Ligand information

SELEX ligand

This entry represents protein P from hepatitis B virus. Protein P is a multifunctional enzyme that converts the viral RNA genome into dsDNA in viral cytoplasmic capsids.-----From Pfam

Name	Uniprot ID	Pfam	MW	Amino acids sequences	PDB	Gene ID
Hepatitis B virus (HBV) polymerase (P protein) (miniP)	Q9QMN7	IPR037531	94.48 kDa	MPLSYQHFRKLLLLDDEAGPLEEELPRLADEGLNRRVAEDLNLGNLNVSIPWTHKVGNFTGLYSSTVPVFNPDWQTPSFPHIHLKEDIINRCQQYVGPLTVNEKRRLKLIMPARFYPNLTKYLPLDKGIKPYYPEHIVNHYFQTRHYLHTLWKAGILYKRETTRSASFCGSPYSWEQELQHGRLVFQTSTRHGDESFCSQSSGILSRSPVGPGIRSQFKQSRLGLQPQQGSMASGTPGRSGIIRARVHSTTRQSFGVEPSGSGHIDSSTSSASSCLHQSAVRKTAYSHLSTSKRQSSSGHAVELQHIPPSSTRSQSEGPILSCWWLQFRNSKPCSDYCLSHIVNLLEDWGPCTEYGEHHIRIPRTPARVTGGVFLVDKNPHNTTESRLVVDFSQFSRGSTHVSWPKFAVPNLQSLTNLLSSNLSWLSLDVSAAFYHLPLHPAAMPHLLVGSSGLPRYVARLSSXSRXINXQHXTMQBLHDSCSRNLYVSLXLLYKTXGRKLHLYSHPIILGFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSVQHLDSLFTAVTNFLLSLGIHLNPTKTKRWGYTLNFMGYVIGSWGTLPQEHIVHKIKHCFRKLPINRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYACIQAKQAFTFSPTYKAFLXXQYLNLYPVARQRSGLCQVFADATPTGWGLAIGHQRMRGTFVXPLPIHTAELLAACFARSRSGAKLIGTDNSVVLSRKYTSFPWLLGCAANWILRGTSFVYVPSALNPADDPSRGRLGLYRPLLRLPYRPTTGRTSLYADSPSVPSHLPDRVHFASPLHVAWRPP	NA	AB031265

Some isolated sequences bind to the affinity of the protein.

Name	Sequence	Ligand	Affinity
S9	5'-UGUUCAUGUCCUACUGUUCAAACAAAAAAACUGUGCACAAAAAUAAAUUGGGGCAUGGACA-3'	HBV P protein	NA
S6	5'-UGUUCAUGUCCUACUGUUCACAGAAAAUAGCUGUGCAAAAAAAAAAGAUGGGGCAUGGACA-3'	HBV P protein	NA

References

[1] A SELEX-screened aptamer of human hepatitis B virus RNA encapsidation signal suppresses viral replication.
Feng, H., Beck, J., Nassal, M., & Hu, K. H.
PloS one, 6(11), e27862. (2011)